Variant report

Variant	rs1000708
Chromosome Location	chr12:60083488-60083489
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10437957	0.82[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs10783999	0.93[ASW][hapmap];0.82[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs11173156	0.85[EUR][1000 genomes]
rs12426819	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1693596	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1693609	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1795886	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2132872	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2464685	0.84[EUR][1000 genomes]
rs2706285	0.91[CHB][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2706299	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2706301	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[EUR][1000 genomes]
rs2711657	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2711666	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[EUR][1000 genomes]
rs4405356	0.84[EUR][1000 genomes]
rs995343	0.88[CEU][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv899131	chr12:59942122-60124089	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv3365928	chr12:60042531-60343212	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv2829972	chr12:60079404-60111653	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1000708	COQ10A	cis	parietal	SCAN
rs1000708	GLI1	cis	cerebellum	SCAN
rs1000708	METTL7B	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:60026600-60089200	Weak transcription	Gastric	stomach
2	chr12:60045800-60085400	Weak transcription	NHDF-Ad	bronchial
3	chr12:60045800-60099800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:60050800-60098600	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr12:60062200-60085800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:60069600-60131400	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr12:60071600-60098600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr12:60072200-60098600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr12:60072400-60085800	Weak transcription	Primary T cells from cord blood	blood
10	chr12:60072600-60085000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:60072800-60098000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr12:60073000-60085000	Weak transcription	Primary B cells from cord blood	blood
13	chr12:60073000-60089000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:60073200-60084400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:60078600-60085200	Weak transcription	Left Ventricle	heart
16	chr12:60078600-60085800	Weak transcription	Aorta	Aorta
17	chr12:60082800-60084400	Enhancers	Fetal Heart	heart
18	chr12:60083000-60083600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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